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Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1

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Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1 Article Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1 Graphical Abstract Authors Jill E. Chrencik, Christopher B. Roth, Masahiko Terakado, ..., Jerold Chun, Raymond C. Stevens, Michael A. Hanson Correspondence [email protected] In Brief Structural analyses of a human lysophosphatidic acid receptor reveal plasticity in ligand recognition and suggest mechanisms for modulation of receptors with distinct functions by common ligand scaffolds. Highlights Accession Numbers d LPA1 structure determined with a selective antagonist 4Z34 4Z35 d Structure-based design led to antagonists with improved 4Z36 characteristics d The LPA1 binding pocket permits extracellular ligand access unlike related S1P1R d Structural analysis predicts metabolic products of cannabinoid ligands bind to LPA1 Chrencik et al., 2015, Cell 161, 1633–1643 June 18, 2015 ª2015 Elsevier Inc. http://dx.doi.org/10.1016/j.cell.2015.06.002 Article Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1 Jill E. Chrencik,1,10 Christopher B. Roth,1 Masahiko Terakado,2 Haruto Kurata,2 Rie Omi,2 Yasuyuki Kihara,5 Dora Warshaviak,3 Shinji Nakade,6 Guillermo Asmar-Rovira,1 Mauro Mileni,1,9 Hirotaka Mizuno,5,6 Mark T. Griffith,1 Caroline Rodgers,1 Gye Won Han,4 Jeffrey Velasquez,4 Jerold Chun,5,8 Raymond C. Stevens,4,7,8 and Michael A. Hanson1,8,11,* 1Department of Structural Discovery, Receptos, San Diego, CA 92121, USA 2Medicinal Chemistry Research Laboratories, Ono Pharmaceutical Co., Ltd., Osaka 618-8585, Japan 3Schro¨ dinger Inc., 120 West 45th Street, New York, NY 10036, USA 4Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA 5Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA 6Exploratory Research Laboratories, Ono Pharmaceutical Co., Ltd., Ibaraki 300-4247, Japan 7iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai, 201210, China 8Co-senior author 9Present Address: Abilita Bio, Inc., San Diego, CA 92121 10Present Address: Structural Biology and Biophysics, Pfizer Inc, Groton, CT 06340 11Present Address: GPCR Consortium, San Marcos, CA 92078 *Correspondence: [email protected] http://dx.doi.org/10.1016/j.cell.2015.06.002 SUMMARY with varied fatty acid chain length and saturation. LPA is present in nearly all cells, tissues, and fluids of the body (Mirendil et al., Lipid biology continues to emerge as an area of sig- 2013) and its effects are mediated by cognate cell-surface G pro- nificant therapeutic interest, particularly as the result tein-coupled receptors (GPCRs) consisting of six family mem- of an enhanced understanding of the wealth of bers designated LPA1-LPA6 (Kihara et al., 2014) that couple to signaling molecules with diverse physiological heterotrimeric G protein complexes to activate downstream properties. This growth in knowledge is epitomized signaling pathways. Targeted deletion of the LPA receptors by lysophosphatidic acid (LPA), which functions has revealed physiological effects on every organ system exam- ined thus far, with receptor dysregulation linked to a range of dis- through interactions with at least six cognate G pro- ease indications including hydrocephalus (Yung et al., 2011), tein-coupled receptors. Herein, we present three infertility (Ye et al., 2005), fibrosis (Tager et al., 2008), pain (Inoue crystal structures of LPA1 in complex with antagonist et al., 2004), and cancer (Mills and Moolenaar, 2003). Three of the tool compounds selected and designed through six LPA receptors, including LPA1 (Kihara et al., 2014), are part of structural and stability analyses. Structural analysis a larger lysophospholipid receptor family (the EDG family) that in- combined with molecular dynamics identified a basis cludes the sphingosine 1-phosphate (S1P) receptors, of which for ligand access to the LPA1 binding pocket from the the structure of one member (S1P1) has been reported (Hanson extracellular space contrasting with the proposed et al., 2012). The closely related cannabinoid receptor CB1 access for the sphingosine 1-phosphate receptor. (Hecht et al., 1996; Matsuda et al., 1990) interacts with endoge- nous ligands structurally related to LPA raising the question of Characteristics of the LPA1 binding pocket raise the possibility of promiscuous ligand recognition of potential polypharmacology between the two receptors, effec- tively connecting these signaling systems. Additional structural phosphorylated endocannabinoids. Cell-based as- details for this family will improve our understanding of their says confirmed this hypothesis, linking the distinct associated function and physiology. receptor systems through metabolically related li- gands with potential functional and therapeutic im- RESULTS plications for treatment of disease. Design of LPA1 Ligands for Structural Studies INTRODUCTION A key for success in GPCR structure determination is the identi- fication of a ligand that stabilizes the receptor into a single and Lysophosphatidic acid (LPA) is a pleiotropic bioactive lipid pro- stable conformation. To facilitate finding such a ligand, a stability duced from extracellular lysophospholipids by autotaxin (ATX), assay based on analytical size exclusion chromatography as well as derived from membrane glycerophospholipids by (aSEC) was developed and used to screen a library of com- phospholipases (Aoki, 2004; Hishikawa et al., 2014; Perrakis pounds (Figure S1). The compound used for initial studies of and Moolenaar, 2014), to produce a range of chemical species LPA1, ONO-9780307 (Table S1, Figure S5A and Supplemental Cell 161, 1633–1643, June 18, 2015 ª2015 Elsevier Inc. 1633 Figure 1. The Overall Structure of LPA1 Colored by Region and Compound Struc- ture in the Bioactive Conformation (A) The ligand ONO-9780307, shown with green carbons, demarcates the binding pocket, which is partially occluded by an N-terminal alpha helix (red) packing closely against the extracellular loops, ECL1 and ECL2 (orange). There are three native disulfide bonds in the extracellular region, one of which constrains the N-terminal capping helix to ECL2. (B) The bioactive conformation of ONO-9780307 in green carbons with high torsional strain energy required for positioning the indane ring adjacent to the dimethoxy phenyl ring. Release of this strain with an optimal torsion angle would result in a clash with the binding pocket. Experimental Procedures), was selected from this library based response to LPA concentration in a calcium mobilization assay on the initial SEC stability assay data (Figure S1)(Tanaka et al., (Figure 2B). To reduce conformational heterogeneity, bRIL was 2011). This assay was used in place of the more traditional modified by replacing a disordered loop with a short linker CPM assay (Alexandrov et al., 2008) to allow early access to sta- (mbRIL). Crystals of dsLPA1-mbRIL in complex with ONO- bility data without the need for pure receptor protein. Using in- 3080573 were grown in a LCP cholesterol mixture and diffracted sights gained from the initial structure, several analogs of ONO-9780307 were designed by considering lipophilicity, struc- tural diversity, and potential metabolic stability. These analogs were synthesized (Supplemental Experimental Procedures), tested for stability induction, and used to generate additional co-crystal structures (Table S1). The design feature of ONO- 9910539 (Figure S5B) is an acetyl group for enhanced polar inter- actions and reduced lipophilicity. The design of ONO-3080573 (Figure S3B) replaced a methylene and the pyrrole ring with an ether and phenyl ring, respectively, to both reduce torsional strain and increase structural diversity and potential metabolic stability. Structure Determination of LPA1-ONO-9780307, LPA1-ONO-9910539, and LPA1-ONO-3080573 To facilitate crystallization, a thermostabilized b562RIL (bRIL) (Chun et al., 2012), was inserted into the third intracellular loop (3IL) at Ballesteros index positions 5.66 (R233) and 6.24 (R247) (Ballesteros and Weinstein, 1995), and thirty-eight residues were truncated from the carboxyl terminus (C terminus). With this engineered construct (LPA1-bRIL) in complex with com- pounds ONO-9780307 and ONO-9910539, crystals were pro- duced in LCP supplemented with cholesterol that diffracted to Figure 2. Generation of the Disulfide Engineered LPA1 (dsLPA1- a final resolution of 3.0 A˚ and 2.9 A˚ , respectively, and supported mbRIL) Crystallization Construct (A) Prediction of cysteine mutants replacing Asp2045.37 and Val2826.59 at the structure solution (Figure 1A). Despite similar stability induction tip of TMV and VI, respectively. for ONO-3080573 (Figure S1), we were unable to crystallize (B) Functional analysis of dsLPA1 and full-length wild-type LPA1 through a this compound with the original LPA1-bRIL construct. In order calcium mobilization assay measured in response to LPA. The EC50 value of to further improve stability and reduce conformational heteroge- the stabilized receptor (994 nM) is about 6-fold higher compared to wild-type neity for crystallization in the presence of ONO-3080573, a series (153 nM). Data are presented as a mean (±SEM, n = 3). of disulfide bonds were engineered into various sites within the (C) Thermal stability analysis of dsLPA1-bRIL compared to the non-engineered crystallization construct LPA1-bRIL. The engineered disulfide bond increases extracellular half of
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